Publications

@article{DBLP:journals/bioinformatics/SinghWH21,

title = {Scalable machine learning-assisted model exploration and inference 

 using Sciope},

author = {Prashant Singh and Fredrik Wrede and Andreas Hellander},

url = {https://doi.org/10.1093/bioinformatics/btaa673},

doi = {10.1093/BIOINFORMATICS/BTAA673},

year  = {2021},

date = {2021-01-01},

journal = {Bioinform.},

volume = {37},

number = {2},

pages = {279–281},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bioinformatics/JiangJGMRSWYDHP21,

title = {Epidemiological modeling in StochSS Live!},

author = {Richard M. Jiang and Bruno Jacob and Matthew Geiger and Sean Matthew and Bryan Rumsey and Prashant Singh and Fredrik Wrede and Tau-Mu Yi and Brian Drawert and Andreas Hellander and Linda R. Petzold},

url = {https://doi.org/10.1093/bioinformatics/btab061},

doi = {10.1093/BIOINFORMATICS/BTAB061},

year  = {2021},

date = {2021-01-01},

journal = {Bioinform.},

volume = {37},

number = {17},

pages = {2787–2788},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bmcbi/JiangWSHP21,

title = {Accelerated regression-based summary statistics for discrete stochastic 

 systems via approximate simulators},

author = {Richard M. Jiang and Fredrik Wrede and Prashant Singh and Andreas Hellander and Linda R. Petzold},

url = {https://doi.org/10.1186/s12859-021-04255-9},

doi = {10.1186/S12859-021-04255-9},

year  = {2021},

date = {2021-01-01},

journal = {BMC Bioinform.},

volume = {22},

number = {1},

pages = {339},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2102-06521,

title = {Robust and integrative Bayesian neural networks for likelihood-free 

 parameter inference},

author = {Fredrik Wrede and Robin Eriksson and Richard M. Jiang and Linda R. Petzold and Stefan Engblom and Andreas Hellander and Prashant Singh},

url = {https://arxiv.org/abs/2102.06521},

year  = {2021},

date = {2021-01-01},

journal = {CoRR},

volume = {abs/2102.06521},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2103-00148,

title = {Scalable federated machine learning with FEDn},

author = {Morgan Ekmefjord and Addi Ait-Mlouk and Sadi Alawadi and Mattias Åkesson and Desislava Stoyanova and Ola Spjuth and Salman Toor and Andreas Hellander},

url = {https://arxiv.org/abs/2103.00148},

year  = {2021},

date = {2021-01-01},

journal = {CoRR},

volume = {abs/2103.00148},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/f1000research/SpjuthCCLSNSETFNMHKHKL21,

title = {Approaches for containerized scientific workflows in cloud environments 

 with applications in life science},

author = {Ola Spjuth and Marco Capuccini and Matteo Carone and Anders Larsson and Wesley Schaal and Jon Ander Novella and Oliver Stein and Morgan Ekmefjord and Paolo Di Tommaso and Evan W. Floden and Cédric Notredame and Pablo A. Moreno and Andreas Hellander and Payam Emami Khoonsari and Stephanie Herman and Kim Kultima and Samuel Lampa},

url = {https://doi.org/10.12688/f1000research.53698.1},

doi = {10.12688/F1000RESEARCH.53698.1},

year  = {2021},

date = {2021-01-01},

journal = {F1000Research},

volume = {10},

pages = {513},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2101-03844,

title = {Understanding the Quality of Container Security Vulnerability Detection 

 Tools},

author = {Omar Javed and Salman Toor},

url = {https://arxiv.org/abs/2101.03844},

year  = {2021},

date = {2021-01-01},

journal = {CoRR},

volume = {abs/2101.03844},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2112-10127,

title = {Proactive Autoscaling for Edge Computing Systems with Kubernetes},

author = {Li Ju and Prashant Singh and Salman Toor},

url = {https://arxiv.org/abs/2112.10127},

year  = {2021},

date = {2021-01-01},

journal = {CoRR},

volume = {abs/2112.10127},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2109-03769,

title = {Training Algorithm Matters for the Performance of Neural Network Potential},

author = {Yunqi Shao and Florian M. Dietrich and Carl Nettelblad and Chao Zhang},

url = {https://arxiv.org/abs/2109.03769},

year  = {2021},

date = {2021-01-01},

journal = {CoRR},

volume = {abs/2109.03769},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{spjuth2021machine,

title = {The machine learning life cycle and the cloud: implications for drug discovery},

author = {Ola Spjuth and Jens Frid and Andreas Hellander},

year  = {2021},

date = {2021-01-01},

journal = {Expert opinion on drug discovery},

volume = {16},

number = {9},

pages = {1071–1079},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2001-10865,

title = {Smart Resource Management for Data Streaming using an Online Bin-packing 

 Strategy},

author = {Oliver Stein and Ben Blamey and Johan Karlsson and Alan Sabirsh and Ola Spjuth and Andreas Hellander and Salman Toor},

url = {https://arxiv.org/abs/2001.10865},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2001.10865},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2001-11760,

title = {Convolutional Neural Networks as Summary Statistics for Approximate 

 Bayesian Computation},

author = {Mattias Åkesson and Prashant Singh and Fredrik Wrede and Andreas Hellander},

url = {https://arxiv.org/abs/2001.11760},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2001.11760},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2012-09579,

title = {Towards Smart e-Infrastructures, A Community Driven Approach Based 

 on Real Datasets},

author = {Prashant Singh and Mona Mohamed Elamin and Salman Toor},

url = {https://arxiv.org/abs/2012.09579},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2012.09579},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2003-11087,

title = {Bootstrapping Weakly Supervised Segmentation-free Word Spotting through 

 HMM-based Alignment},

author = {Tomas Wilkinson and Carl Nettelblad},

url = {https://arxiv.org/abs/2003.11087},

year  = {2020},

date = {2020-01-01},

journal = {CoRR},

volume = {abs/2003.11087},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bioinformatics/WredeH19,

title = {Smart computational exploration of stochastic gene regulatory network 

 models using human-in-the-loop semi-supervised learning},

author = {Fredrik Wrede and Andreas Hellander},

url = {https://doi.org/10.1093/bioinformatics/btz420},

doi = {10.1093/BIOINFORMATICS/BTZ420},

year  = {2019},

date = {2019-01-01},

journal = {Bioinform.},

volume = {35},

number = {24},

pages = {5199–5206},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1901-07335,

title = {Adapting The Secretary Hiring Problem for Optimal Hot-Cold Tier Placement 

 under Top-K Workloads},

author = {Ben Blamey and Fredrik Wrede and Johan Karlsson and Andreas Hellander and Salman Toor},

url = {http://arxiv.org/abs/1901.07335},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1901.07335},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1912-09088,

title = {Resource- and Message Size-Aware Scheduling of Stream Processing at 

 the Edge with application to Realtime Microscopy},

author = {Ben Blamey and Ida-Maria Sintorn and Andreas Hellander and Salman Toor},

url = {http://arxiv.org/abs/1912.09088},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1912.09088},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/peerj-cs/CapucciniLCNSGT19,

title = {On-demand virtual research environments using microservices},

author = {Marco Capuccini and Anders Larsson and Matteo Carone and Jon Ander Novella and Noureddin Sadawi and Jianliang Gao and Salman Toor and Ola Spjuth},

url = {https://doi.org/10.7717/peerj-cs.232},

doi = {10.7717/PEERJ-CS.232},

year  = {2019},

date = {2019-01-01},

journal = {PeerJ Comput. Sci.},

volume = {5},

pages = {e232},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1910-14029,

title = {Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline},

author = {Jing Liu and Stefan Engblom and Carl Nettelblad},

url = {http://arxiv.org/abs/1910.14029},

year  = {2019},

date = {2019-01-01},

journal = {CoRR},

volume = {abs/1910.14029},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2018multi,

title = {Multi-statistic approximate Bayesian computation with multi-armed bandits},

author = {Prashant Singh and Andreas Hellander},

year  = {2018},

date = {2018-01-01},

journal = {arXiv preprint arXiv:1805.08647},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/bmcbi/AusmeesJTHN18,

title = {BAMSI: a multi-cloud service for scalable distributed filtering 

 of massive genome data},

author = {Kristiina Ausmees and Aji John and Salman Zubair Toor and Andreas Hellander and Carl Nettelblad},

url = {https://doi.org/10.1186/s12859-018-2241-z},

doi = {10.1186/S12859-018-2241-Z},

year  = {2018},

date = {2018-01-01},

journal = {BMC Bioinform.},

volume = {19},

number = {1},

pages = {240:1–240:11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1805-08647,

title = {Multi-Statistic Approximate Bayesian Computation with Multi-Armed 

 Bandits},

author = {Prashant Singh and Andreas Hellander},

url = {http://arxiv.org/abs/1805.08647},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1805.08647},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1807-07724,

title = {Apache Spark Streaming and HarmonicIO: A Performance and Architecture 

 Comparison},

author = {Ben Blamey and Andreas Hellander and Salman Zubair Toor},

url = {http://arxiv.org/abs/1807.07724},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1807.07724},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/jcheminf/AhmedGCTSLS18,

title = {Efficient iterative virtual screening with Apache Spark and conformal 

 prediction},

author = {Laeeq Ahmed and Valentin Georgiev and Marco Capuccini and Salman Zubair Toor and Wesley Schaal and Erwin Laure and Ola Spjuth},

url = {https://doi.org/10.1186/s13321-018-0265-z},

doi = {10.1186/S13321-018-0265-Z},

year  = {2018},

date = {2018-01-01},

journal = {J. Cheminformatics},

volume = {10},

number = {1},

pages = {8:1–8:8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/tsc/OsmaniTKKLWKET18,

title = {Secure Cloud Connectivity for Scientific Applications},

author = {Lirim Osmani and Salman Toor and Miika Komu and Matti J. Kortelainen and Tomas Lindén and John White and Rasib Hassan Khan and Paula Eerola and Sasu Tarkoma},

url = {https://doi.org/10.1109/TSC.2015.2469292},

doi = {10.1109/TSC.2015.2469292},

year  = {2018},

date = {2018-01-01},

journal = {IEEE Trans. Serv. Comput.},

volume = {11},

number = {4},

pages = {658–670},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1805-06180,

title = {KubeNow: an On-Demand Cloud-Agnostic Platform for Microservices-Based 

 Research Environments},

author = {Marco Capuccini and Anders Larsson and Matteo Carone and Jon Ander Novella and Noureddin Sadawi and Jianliang Gao and Salman Zubair Toor and Ola Spjuth},

url = {http://arxiv.org/abs/1805.06180},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1805.06180},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1808-02318,

title = {MaRe: Container-Based Parallel Computing with Data Locality},

author = {Marco Capuccini and Salman Zubair Toor and Staffan Arvidsson and Ola Spjuth},

url = {http://arxiv.org/abs/1808.02318},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1808.02318},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-1804-06724,

title = {Using Convex Optimization of Autocorrelation with Constrained Support 

 and Windowing for Improved Phase Retrieval Accuracy},

author = {Alberto Pietrini and Carl Nettelblad},

url = {http://arxiv.org/abs/1804.06724},

year  = {2018},

date = {2018-01-01},

journal = {CoRR},

volume = {abs/1804.06724},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017sequential,

title = {A sequential sampling strategy for adaptive classification of computationally expensive data},

author = {Prashant Singh and Joachim van der Herten and Dirk Deschrijver and Ivo Couckuyt and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {Structural and Multidisciplinary Optimization},

volume = {55},

pages = {1425–1438},

publisher = {Springer Berlin Heidelberg},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017constrained,

title = {Constrained multi-objective antenna design optimization using surrogates},

author = {Prashant Singh and Marco Rossi and Ivo Couckuyt and Dirk Deschrijver and Hendrik Rogier and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {International Journal of Numerical Modelling: Electronic Networks, Devices and Fields},

volume = {30},

number = {6},

pages = {e2248},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{singh2017multi,

title = {Multi-objective geometry optimization of a gas cyclone using triple-fidelity co-kriging surrogate models},

author = {Prashant Singh and Ivo Couckuyt and Khairy Elsayed and Dirk Deschrijver and Tom Dhaene},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Optimization Theory and Applications},

volume = {175},

pages = {172–193},

publisher = {Springer US},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/siamam/HellanderKLM17,

title = {Robustness Analysis of Spatiotemporal Models in the Presence of Extrinsic 

 Fluctuations},

author = {Andreas Hellander and Jan Klosa and Per Lötstedt and Shev MacNamara},

url = {https://doi.org/10.1137/15M1052317},

doi = {10.1137/15M1052317},

year  = {2017},

date = {2017-01-01},

journal = {SIAM J. Appl. Math.},

volume = {77},

number = {4},

pages = {1157–1183},

keywords = {},

pubstate = {published},

tppubtype = {article}

}